ArticleNucleic acids research2017
sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- FragmentFinder-a user-friendly, Windows-based tool for identifying and characterizing short RNAs excised from any noncoding RNA.NAR genomics and bioinformatics · 2026Article
- Identification of differentially expressed non-coding RNAs in the plasma of women with preterm birth.RNA biology · 2025Article
- Intratumoral core microbiota predicts prognosis and therapeutic response in gastrointestinal cancers.Microbiology spectrum · 2025Article
- Differential 5'-tRNA Fragment Expression in Circulating Preeclampsia Syncytiotrophoblast Vesicles Drives Macrophage Inflammation.Hypertension (Dallas, Tex. : 1979) · 2024Article
- sRNAflow: A Tool for the Analysis of Small RNA-Seq Data.Non-coding RNA · 2024Article
- Engineering a tunable micropattern-array assay to sort single extracellular vesicles and particles to detect RNA and protein in situ.Journal of extracellular vesicles · 2023Article
- Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX)-deficient Arabidopsis inflorescence.Scientific data · 2023Article
- Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts.Bioinformatics (Oxford, England) · 2023Article
- Men who inject opioids exhibit altered tRNA-Gly-GCC isoforms in semen.Molecular human reproduction · 2023Article
- mtR_find: A Parallel Processing Tool to Identify and Annotate RNAs Derived from the Mitochondrial Genome.International journal of molecular sciences · 2023Article
- Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking.International journal of molecular sciences · 2023Article
- BIC: a database for the transcriptional landscape of bacteria in cancer.Nucleic acids research · 2023Article
- Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy.Frontiers in bioinformatics · 2023Article
- tiny-count: a counting tool for hierarchical classification and quantification of small RNA-seq reads with single-nucleotide precision.Bioinformatics advances · 2023Article
- A Novel PiRNA Enhances CA19-9 Sensitivity for Pancreatic Cancer Identification by Liquid Biopsy.Journal of clinical medicine · 2022Article
- NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis.Nature communications · 2022Article
- ITAS: Integrated Transcript Annotation for Small RNA.Non-coding RNA · 2022Article
- The Multiverse of Plant Small RNAs: How Can We Explore It?International journal of molecular sciences · 2022Review
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues.Scientific data · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) measurement results across different platforms, miRNA mapping associated with miRNA sequence variation (isomiR) and RNA editing, and the origin of those unmapped reads after screening against all endogenous reference sequence databases. To address these issues, we built a comprehensive and customizable sRNA-Seq data analysis pipeline-sRNAnalyzer, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation. We evaluated our pipeline on both artificial samples (including synthetic miRNA and Escherichia coli cultures) and biological samples (human tissue and plasma). sRNAnalyzer is implemented in Perl and available at: http://srnanalyzer.systemsbiology.net/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.